Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
18.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.60, Jaccard 0.47, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.704 kcal/mol/HA)
✓ Good fit quality (FQ -6.86)
✓ Good H-bonds (4 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Moderate strain (18.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (20)
Score
-21.825
kcal/mol
LE
-0.704
kcal/mol/HA
Fit Quality
-6.86
FQ (Leeson)
HAC
31
heavy atoms
MW
420
Da
LogP
5.65
cLogP
Interaction summary
HB 4
HY 16
PI 0
CLASH 2
Interaction summary
HB 4
HY 16
PI 0
CLASH 2
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 3.230 | Score | -21.825 |
|---|---|---|---|
| Inter norm | -0.725 | Intra norm | 0.021 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 4 |
| Artifact reason | geometry warning; 20 clashes; 1 protein clash | ||
| Residues |
ARG22
ARG342
CYS26
GLN341
GLU343
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
THR21
THR285
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG22
ARG242
ARG337
ARG342
ASP243
ASP385
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
SER282
THR241
| ||
| Current overlap | 9 | Native recall | 0.60 |
| Jaccard | 0.47 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:ORX602
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 432 | 1.2819667923104754 | -1.07349 | -31.6975 | 4 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 508 | 1.4997382959729062 | -0.884852 | -27.6653 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 515 | 1.5254808840833125 | -0.881438 | -27.5456 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 454 | 1.9448945471273054 | -0.810123 | -19.1083 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 437 | 2.1596452852315497 | -1.03103 | -30.8386 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 491 | 2.1910489273537 | -0.662632 | -20.132 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 462 | 2.494395741736802 | -1.13889 | -33.7078 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 445 | 2.728551198212635 | -0.743102 | -21.4543 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 470 | 2.873293646185988 | -0.833854 | -25.7642 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 466 | 3.2298751185699697 | -0.724965 | -21.8245 | 4 | 13 | 9 | 0.60 | 0.00 | - | no | Current |
| 505 | 3.6090669749400317 | -0.727024 | -22.2334 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.825kcal/mol
Ligand efficiency (LE)
-0.7040kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.859
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
420.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.65
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
100.50kcal/mol
Minimised FF energy
81.60kcal/mol
SASA & burial
✓ computed
SASA (unbound)
635.3Ų
Total solvent-accessible surface area of free ligand
BSA total
472.9Ų
Buried surface area upon binding
BSA apolar
339.2Ų
Hydrophobic contacts buried
BSA polar
133.7Ų
Polar contacts buried
Fraction buried
74.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2452.9Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1379.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)